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<title>MSROLL - Prepare Job | WICE</title>
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            <h1><a href="/" title="Web-based Interactive Computational Environment Homepage">
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            <p>Web-based Interactive Computational Environment</p>
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                        <li id="nav-msroll" class="tool"><a href="msroll.html" title="Setup and run the MSROLL utility"
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                                Generate a 3D mesh from an x-ray crystallography experiment
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                                Optimize a 3D MSROLL mesh by reducing the number of triangles
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                                Calculate the hydrodynamic transport tensors from the 3D structure of a molecule
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            <span class="working-project">Current Project:
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        <h1>Prepare MSROLL Job</h1>
        <form action="msroll-result.html" method="post" class="tool-setup">
            <div class="controls">
                <input type="submit" value="Store" name="action" class="store" title="Save these job parameters for future execution">
                <input type="submit" value="Execute" name="action" title="Run this job now">
            </div>
            <div id="job-details">
                <div class="meta field toggle">
                    <label for="save-job" class="optional">Save Job</label>
                    <input name="save" id="save-job" type="checkbox" checked>
                </div>
                <div class="meta field">
                    <label for="project">Project Name</label>
                    <span class="autocomplete-browser projects" title="Enter the name of an existing project, or a name for a new one">
                        <input name="project" class="projects" id="project" placeholder="No Project" size="25" value="Example">
                        <a href="/user/browse/projects" class="projects" title="Available projects" rel="Projects">
                            <span>Browse</span>
                        </a>
                    </span>
                </div>
                <div class="meta field">
                    <label for="job-name" class="optional">Job Name</label>
                    <span class="autocomplete-browser" title="Enter the name of a new job, or recall a previously stored one">
                        <input name="job" class="msroll-jobs" id="job-name" placeholder="Automatic" size="25" value="1ubq201">
                        <a href="/user/browse/jobs/msroll" class="msroll-jobs" title="Previously stored MSROLL jobs" rel="~/example">
                            <span>Browse</span>
                        </a>
                    </span>
                </div>
            </div>
            <div class="warning ui-state-error">
                <strong><span class="ui-icon ui-icon-alert"></span>Warning:</strong>
                You have already run the MSROLL tool on this job. You should
                <a href="">archive</a> the previous results or they will be lost.
            </div>
            <fieldset id="structure-parameteres" class="parameters">
                <legend>Input Structure</legend>
                <div class="method-selection">
                    <input type="radio" name="structure_type" id="structure-upload-select" value="upload">
                    <label for="structure-upload-select" title="Upload a structure from your computer to process with MSROLL">
                        Upload a Structure
                    </label>
                    <input type="radio" name="structure_type" id="structure-existing-select" value="existing" checked>
                    <label for="structure-existing-select" title="Use a structure stored in your user account in MSROLL">
                        Use an Existing Structure
                    </label>
                    <input type="radio" name="structure_type" id="structure-pdb-select" value="pdb">
                    <label for="structure-pdb-select" title="Process a PDB file from the protein databank in MSROLL">
                        Use a PDB File
                    </label>
                </div>
                <div id="structure-upload" class="upload options">
                    <label for="structure-upload-file" title="Select a file to be uploaded from your computer and processed with MSROLL">
                        Structure File:
                        <input type="file" name="structure_upload" id="structure-upload-file">
                    </label>
                    <div class="store-fields">
                        <label for="structure-upload-save" title="If this is selected, the uploaded file will be saved to your user account for future use">
                            <input type="checkbox" name="save_structure" id="structure-upload-save" checked>
                            Store uploaded file
                        </label>
                        <label for="structure-upload-save-name" title="Name to store the uploaded file as on the server. If none is provided the original name will be used.">
                            <abbr title="File name to store structure file as">as</abbr>
                            <input name="save_structure_name" id="structure-upload-save-name" placeholder="original file name">
                        </label>
                    </div>
                    
                </div>
                <div id="structure-existing" class="existing options">
                    <label for="structure-existing-file" title="Select a file to be uploaded from your computer and processed with MSROLL">
                        Existing Structure:
                        <span class="autocomplete-browser" title="Enter the path to an existing structure file on the server">
                            <input name="structure_file" class="structures" id="structure-existing-file" placeholder="Path to structure file" value="example/1ubq.pdb.201.h.pdb">
                            <a href="/user/browse/structures" class="structures" title="Structure files available on server" rel="~/example">
                                <span>Browse</span>
                            </a>
                        </span>
                    </label>
                </div>
                <div id="structure-pdb" class="library options">
                    <label for="structure-pdb-id">
                        <abbr title="Protein Data bank Identifier">PDB ID</abbr>:
                        <input name="structure_pdb" id="structure-pdb-id" size="4">
                        <span class="pdb-title"></span>
                    </label>
                    <p class="note">
                        More information about PDB files can be found in the 
                        <a href="http://www.rcsb.org/pdb/home/home.do" title="Visit the RCSB Protein Data Bank">
                        Protein Data Bank</a>.
                    </p>
                </div>
            </fieldset>
            <fieldset id="radii-parameters" class="parameters">
                <legend>Atomic Radii</legend>
                <div class="method-selection">
                    <input type="radio" name="radii_type" id="radii-default-select" value="default">
                    <label for="radii-default-select" title="Use the default atomic radii">
                        Use Defaults
                    </label>
                    <input type="radio" name="radii_type" id="radii-preset-select" value="preset" checked>
                    <label for="radii-preset-select" title="Use a preset atomic radii file">
                        Use Existing Radii
                    </label>
                    <input type="radio" name="radii_type" id="radii-upload-select" value="upload">
                    <label for="radii-upload-select" title="Upload a custom atomic radii file">
                        Upload Custom Atomic Radii
                    </label>
                </div>
                <div id="radii-default" class="default options">
                    <p>MSROLL's default radius file will be used.</p>
                </div>
                <div id="radii-preset" class="existing options">
                    <label for="radii-exising-file">
                        Existing Radii File:
                        <span class="autocomplete-browser" title="Enter the name of a new job, or recall a previously stored one">
                            <input name="radii_file" class="radii" id="radii-existing-file" placeholder="Path to existing radii file" value="example/radius1.1">
                            <a href="/user/browse/radii" class="radii" title="Radius files available on server" rel="~/example">
                                <span>Browse</span>
                            </a>
                        </span>
                    </label>
                </div>
                <div id="radii-upload" class="upload options">
                    <label for="radii-upload-file" title="Select an atomic radii file to be uploaded from your computer">
                        Radii File:
                        <input type="file" name="radii_upload" id="radii-upload-file">
                    </label>
                    <div class="store-fields">
                        <label for="radii-upload-save" title="If this is selected, the uploaded file will be saved to your user account for future use">
                            <input type="checkbox" name="save_radii" id="radii-upload-save" checked>
                            Store uploaded file
                        </label>
                        <label for="radii-upload-save-name" title="Name to store the uploaded file as on the server. If none is provided the original name will be used.">
                            <abbr title="File name to store radii file as">as</abbr>
                            <input name="save_radii_name" id="radii-upload-save-name" placeholder="original file name">
                        </label>
                    </div>
                </div>
            </fieldset>
            <fieldset id="msroll-parameters" class="tool parameters">
                <legend>MSROLL Parameters</legend>
                <label for="msroll-probe-radius" class="slider" title="MSROLL Probing Radius (Default: 1.5)">
                    <span class="text">Probe Radius: <abbr title="Angstroms" class="units">[&#8491;]</abbr></span>
                    <input name="probe_radius" id="msroll-probe-radius" min="0.1" max="3" size="3" value="1.50" step="0.01">
                </label>
                <label for="msroll-fitness" class="slider" title="MSROLL Triangle Fitness (Default 0.2)">
                    <span class="text">Fitness:</span>
                    <input name="fitness" id="msroll-fitness" min="0.05" max="0.3" size="3" value="0.20" step="0.01">
                </label>
            </fieldset>
            <div class="controls">
                <input type="submit" value="Store" name="action" class="store" title="Save these job parameters for future execution">
                <input type="submit" value="Execute" name="action" title="Run this job now">
            </div>
        </form>
    </div>
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